Someone mentioned guard masterary and parry as well. Samurai doesn't have the single highest parry skill, they're tied with ninja and thf for A- skill, so all 3 jobs should a parry masterary trait in that case.
I'd leave existing NMs alone, but add a few new NMs that could have world wide pops, including expansion zones. Some could be soloable by low/mid/high level players, some could be the difficultly of hard HNMs and such, and everything inbetween.
I'd make a lot of tweaks to thief.
-Nerf perfect dodge to be a normal 10 minute reuse ability that greatly enhances evasion for 30 seconds. And replace it with a treasure hunter enhancing 2hour for the duration of one fight. Preheps making the next mob 50% tops more likely to drop more item, thus increasing chances at rare wanted items. Maybe less than 50%, that's just an idea to start. As a result, certain rare items/crafting materal drops would become more common, increasing supply of many big money items over time, making this game more friendly to people that can't play as often, as well as more friendly to the people with the thief. More Okotes, more bounding boots, more behemoth leather, more god armor for "all", more black belts, more ridills, more coins for AF+1, more....anything in circulation.
Or...I'd just add several more TH+1/TH+2 items to the game. As of now, TH2+2% sounds ok...but +10% would be getting somewhere.
Or...If those ideas don't fly well with people, just give thf A+ in dagger skill. There, problem with thf damage compared to other endgame DDs would be narrowed down a lot.
More status bolts, slow bolts and paralyze bolts.
Enhance DRG jumps to match or surpass what war/drg with GAX and drk/ with scythe do. Give them more reason to need super jump.
Give whm A- club skill
Give brd some job abilities, just for the sake of making it more interesting.
Make the haidiate with 15 dex and 5 haste equippable by thief, enough said.
Make drain arrows, so sam could farm decently. They really need help in that department compared to all the other melees that have some way of getting their hp back without medding. Or a way for them to exchange tp for hp.
Give brd slightly higher sword skill than it is currently.
Make some bongo type instruments, that'd be fun.
Allow for GMs to do something more readily about the more obvious bots/gilsellers.